SWISS-MODEL Repository - Model Details

Model Overview
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1
342

Sequence
UniProt O01609
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
7TM_GPCR_Srd

Model 3D Structure
Model information:
Modelled residue range: 16 to 325
Based on template: [ 2lnl ]  
Sequence Identity [%]: 12%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2lnl): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1         SDTYMN TADSIFVITV TILTSIGFLL NLLLLYLIIW KSPRNLTPYR
2lnlA     29    pc--mletet lnkyvviiay alvfllsllg nslvmlvily -srvgrsvtd
                                                                      
TARGET                      hhhhhhhhh hhhhhhhhhh hhhhhhhhhh         hh
2lnlA                       hhhhhhhhh hhhhhhhhhh hhhhhhhhhh         hh


TARGET    47    IFLANTTITQ LVYALFAVTS MPRVLAKHQY TIVIYLGPVQ FFGEWFSYMS
2lnlA     76    vyllnlalad llfaltlpiw ---------- --aaskvngw ifgtflckvv
                                                                      
TARGET          hhhhhhhhhh hhhh   hss sssss   ss sssss          hhhhhh
2lnlA           hhhhhhhhhh hhhh   hhh              hhhhh        hhhhhh


TARGET    97    YVGILHLSLN SFISLMLSMI YRYFSIRFKR FTANTSIILC IIGYFFPFLI
2lnlA     114   sllkevnfys gilllacisv drylaivhat rtltqkrhlv kfvclgcwgl
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhh            hhhh hhhhhhhhhh
2lnlA           hhhhhhhhhh hhhhhhhhhh hhhhh            hhhh hhhhhhhhhh


TARGET    147   FASCSNIAIS SSLSFNTAVL DGMVENLESY HMVLTTEISN HPSLIILTLA
2lnlA     164   smnlslpffl frqayhpnns spvcyevlgn dtakwrmvlr -------ilp
                                                                      
TARGET          hhh   hhh                      s ss ssss             h
2lnlA           hhhhhhhhhh                             hhhh        hhh


TARGET    197   VTCGLVPIYF VMYWCRHQIH KTLKQTRSVH SPSTRDNARR LVRALTIQSI
2lnlA     207   htfgfivplf vmlfcygftl rtlfk----- --ahmgqkhr amrvifavvl
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh                       hhhhhhhhhh
2lnlA           h   hhhhhh hhhhhhhhhh                       hhhhhhhhhh


TARGET    247   IPLVSVFPAS IFWCLSQLGF VE-------- ---PTMYSYF IIPCLSLGCI
2lnlA     250   ifllcwlpyn lvlladtlmr tqviqescer rnnigralda teilgflhsc
                                                                      
TARGET          hhhhhhhhhh hhhhhhh                      hhh hhhhhhh   
2lnlA           hhhhhhhhhh hhhhhhhh          hhh hhh   hhhh hhhhhhh   


TARGET    286   ADPVVTIRCV LPYRRWILKL CNMST                           
2lnlA     300   lnpiiyafig qnfrhgflki lamhg-                          
                                                                      
TARGET          hhhhhhhh     hhhhhhhh hhh                             
2lnlA           hhhhhhhh     hhhhhhhh hhh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 2lnl is annotated as MONOMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 2lnl.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 12.773) to infer a conservation of the oligomeric state 
 Please use the advancend features of the SwissModel Project Mode 
       
 The target structure was calculated as SINGLE CHAIN

Template Selection 
 - Start SMR-Pipeline for:0636454b6486af2d7cdbf3fcea097f06 on BC2-cluster at Thu Feb 21 03:19:13
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -     *************************************************************************
 - building model based on 2lnlA (16-325) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:0636454b6486af2d7cdbf3fcea097f06 on BC2-cluster at Thu Feb 21 03:20:53
2013


Template Description
Match Chain SeqId

2lnl: STRUCTURE OF HUMAN CXCR1 IN PHOSPHOLIPID BILAYERS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

16-325 2lnlA 13%
[Model]

4grv: THE CRYSTAL STRUCTURE OF THE NEUROTENSIN RECEPTOR NTS1 IN NEUROTENSIN (8-13)
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-315 4grvA 7%
[Model]

3vw7: CRYSTAL STRUCTURE OF HUMAN PROTEASE-ACTIVATED RECEPTOR 1 (WITH ANTAGONIST VORAPAXAR AT 2.2 ANGSTROM
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-312 3vw7A 6%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.